Multiple sequence alignment - TraesCS7D01G423600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G423600 chr7D 100.000 2861 0 0 1 2861 543730888 543733748 0.000000e+00 5284.0
1 TraesCS7D01G423600 chr7D 84.840 686 99 2 1 686 548550426 548551106 0.000000e+00 686.0
2 TraesCS7D01G423600 chr7B 90.287 1359 69 29 608 1927 587101595 587102929 0.000000e+00 1720.0
3 TraesCS7D01G423600 chr7B 89.919 1359 65 30 608 1927 587266811 587268136 0.000000e+00 1685.0
4 TraesCS7D01G423600 chr7B 92.731 963 44 8 991 1927 587479903 587480865 0.000000e+00 1367.0
5 TraesCS7D01G423600 chr7B 94.558 882 42 4 991 1866 587440901 587441782 0.000000e+00 1358.0
6 TraesCS7D01G423600 chr7B 93.018 888 42 3 991 1872 587519164 587520037 0.000000e+00 1279.0
7 TraesCS7D01G423600 chr7B 87.988 691 66 9 1 675 569440653 569439964 0.000000e+00 800.0
8 TraesCS7D01G423600 chr7B 94.820 444 23 0 991 1434 587615434 587615877 0.000000e+00 693.0
9 TraesCS7D01G423600 chr7B 90.787 521 28 5 1427 1927 587620573 587621093 0.000000e+00 678.0
10 TraesCS7D01G423600 chr7B 87.467 383 22 15 610 989 587479499 587479858 4.410000e-113 418.0
11 TraesCS7D01G423600 chr7B 87.139 381 23 15 610 987 587518760 587519117 2.650000e-110 409.0
12 TraesCS7D01G423600 chr7B 92.381 210 15 1 2183 2392 587635703 587635911 5.990000e-77 298.0
13 TraesCS7D01G423600 chr7B 85.417 288 27 11 1946 2226 587103025 587103304 4.670000e-73 285.0
14 TraesCS7D01G423600 chr7B 85.121 289 26 9 1946 2226 587268232 587268511 2.170000e-71 279.0
15 TraesCS7D01G423600 chr7B 86.220 254 20 8 2244 2491 587103293 587103537 7.860000e-66 261.0
16 TraesCS7D01G423600 chr7B 85.827 254 21 8 2244 2491 587268500 587268744 3.660000e-64 255.0
17 TraesCS7D01G423600 chr7B 85.490 255 21 8 2244 2491 587520273 587520518 4.730000e-63 252.0
18 TraesCS7D01G423600 chr7B 86.585 246 11 5 2635 2858 587520775 587521020 4.730000e-63 252.0
19 TraesCS7D01G423600 chr7B 86.235 247 12 5 2634 2858 587442724 587442970 6.120000e-62 248.0
20 TraesCS7D01G423600 chr7B 86.179 246 12 5 2635 2858 587103795 587104040 2.200000e-61 246.0
21 TraesCS7D01G423600 chr7B 85.830 247 13 5 2634 2858 587482051 587482297 2.850000e-60 243.0
22 TraesCS7D01G423600 chr7B 85.366 246 14 5 2635 2858 587269001 587269246 4.770000e-58 235.0
23 TraesCS7D01G423600 chr7B 87.736 212 9 11 778 989 587440662 587440856 6.160000e-57 231.0
24 TraesCS7D01G423600 chr7B 85.427 199 15 10 2033 2226 587520095 587520284 8.090000e-46 195.0
25 TraesCS7D01G423600 chr7B 92.857 126 7 1 2487 2610 587103674 587103799 6.300000e-42 182.0
26 TraesCS7D01G423600 chr7B 92.857 126 7 1 2487 2610 587268880 587269005 6.300000e-42 182.0
27 TraesCS7D01G423600 chr7B 92.857 126 7 1 2487 2610 587520654 587520779 6.300000e-42 182.0
28 TraesCS7D01G423600 chr7B 81.140 228 20 7 2511 2734 587653122 587653330 8.200000e-36 161.0
29 TraesCS7D01G423600 chr7B 91.379 116 10 0 2244 2359 587442157 587442272 2.950000e-35 159.0
30 TraesCS7D01G423600 chr7B 90.991 111 7 2 2502 2610 587481947 587482056 2.300000e-31 147.0
31 TraesCS7D01G423600 chr7B 90.090 111 8 2 2502 2610 587442620 587442729 1.070000e-29 141.0
32 TraesCS7D01G423600 chr7B 83.133 166 11 9 824 989 587615241 587615389 4.970000e-28 135.0
33 TraesCS7D01G423600 chr7B 91.566 83 7 0 2244 2326 587481205 587481287 6.480000e-22 115.0
34 TraesCS7D01G423600 chr7B 97.727 44 1 0 1884 1927 587441782 587441825 3.060000e-10 76.8
35 TraesCS7D01G423600 chr7B 83.146 89 6 7 2135 2221 587635357 587635438 3.950000e-09 73.1
36 TraesCS7D01G423600 chr6B 93.835 957 39 5 991 1927 694681454 694682410 0.000000e+00 1423.0
37 TraesCS7D01G423600 chr6B 92.012 989 50 14 1 989 694680450 694681409 0.000000e+00 1362.0
38 TraesCS7D01G423600 chr6B 85.417 288 27 11 1946 2226 694682506 694682785 4.670000e-73 285.0
39 TraesCS7D01G423600 chr6B 86.220 254 20 8 2244 2491 694682774 694683018 7.860000e-66 261.0
40 TraesCS7D01G423600 chr6B 86.179 246 12 5 2635 2858 694683274 694683519 2.200000e-61 246.0
41 TraesCS7D01G423600 chr6B 92.857 126 7 1 2487 2610 694683153 694683278 6.300000e-42 182.0
42 TraesCS7D01G423600 chr1D 92.864 995 48 13 1 989 110904645 110905622 0.000000e+00 1423.0
43 TraesCS7D01G423600 chr7A 92.641 992 45 12 1 989 625674428 625675394 0.000000e+00 1402.0
44 TraesCS7D01G423600 chr7A 92.634 991 42 13 1 989 625641655 625642616 0.000000e+00 1397.0
45 TraesCS7D01G423600 chr7A 93.963 762 46 0 993 1754 625642659 625643420 0.000000e+00 1153.0
46 TraesCS7D01G423600 chr7A 93.223 782 35 5 991 1754 625675435 625676216 0.000000e+00 1134.0
47 TraesCS7D01G423600 chr7A 86.401 728 69 19 1 725 631653238 631652538 0.000000e+00 769.0
48 TraesCS7D01G423600 chr7A 85.906 298 35 2 432 725 617552301 617552007 7.700000e-81 311.0
49 TraesCS7D01G423600 chr1B 92.542 952 47 15 1 947 169024429 169025361 0.000000e+00 1343.0
50 TraesCS7D01G423600 chr4A 85.424 542 67 6 1 542 141909567 141909038 1.160000e-153 553.0
51 TraesCS7D01G423600 chr2A 83.073 449 39 17 554 984 701783101 701782672 9.680000e-100 374.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G423600 chr7D 543730888 543733748 2860 False 5284.000000 5284 100.000000 1 2861 1 chr7D.!!$F1 2860
1 TraesCS7D01G423600 chr7D 548550426 548551106 680 False 686.000000 686 84.840000 1 686 1 chr7D.!!$F2 685
2 TraesCS7D01G423600 chr7B 569439964 569440653 689 True 800.000000 800 87.988000 1 675 1 chr7B.!!$R1 674
3 TraesCS7D01G423600 chr7B 587620573 587621093 520 False 678.000000 678 90.787000 1427 1927 1 chr7B.!!$F1 500
4 TraesCS7D01G423600 chr7B 587101595 587104040 2445 False 538.800000 1720 88.192000 608 2858 5 chr7B.!!$F3 2250
5 TraesCS7D01G423600 chr7B 587266811 587269246 2435 False 527.200000 1685 87.818000 608 2858 5 chr7B.!!$F4 2250
6 TraesCS7D01G423600 chr7B 587479499 587482297 2798 False 458.000000 1367 89.717000 610 2858 5 chr7B.!!$F6 2248
7 TraesCS7D01G423600 chr7B 587518760 587521020 2260 False 428.166667 1279 88.419333 610 2858 6 chr7B.!!$F7 2248
8 TraesCS7D01G423600 chr7B 587615241 587615877 636 False 414.000000 693 88.976500 824 1434 2 chr7B.!!$F8 610
9 TraesCS7D01G423600 chr7B 587440662 587442970 2308 False 368.966667 1358 91.287500 778 2858 6 chr7B.!!$F5 2080
10 TraesCS7D01G423600 chr6B 694680450 694683519 3069 False 626.500000 1423 89.420000 1 2858 6 chr6B.!!$F1 2857
11 TraesCS7D01G423600 chr1D 110904645 110905622 977 False 1423.000000 1423 92.864000 1 989 1 chr1D.!!$F1 988
12 TraesCS7D01G423600 chr7A 625641655 625643420 1765 False 1275.000000 1397 93.298500 1 1754 2 chr7A.!!$F1 1753
13 TraesCS7D01G423600 chr7A 625674428 625676216 1788 False 1268.000000 1402 92.932000 1 1754 2 chr7A.!!$F2 1753
14 TraesCS7D01G423600 chr7A 631652538 631653238 700 True 769.000000 769 86.401000 1 725 1 chr7A.!!$R2 724
15 TraesCS7D01G423600 chr1B 169024429 169025361 932 False 1343.000000 1343 92.542000 1 947 1 chr1B.!!$F1 946
16 TraesCS7D01G423600 chr4A 141909038 141909567 529 True 553.000000 553 85.424000 1 542 1 chr4A.!!$R1 541

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
989 1029 1.97266 ATCGCTTTCTTCCTCCCCCG 61.973 60.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 2885 0.037326 GGAGGATGACACACTTGCGA 60.037 55.0 0.0 0.0 0.0 5.1 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.203070 GGAGCCATGTACCAGCGG 60.203 66.667 0.00 0.00 0.00 5.52
170 171 2.748605 GAGGTCGCATATCTTCACCAG 58.251 52.381 0.00 0.00 0.00 4.00
363 377 2.601666 AGGACGAGGCTGCACTGA 60.602 61.111 0.50 0.00 0.00 3.41
733 765 3.093172 TGGCCATGGATGCGGGTA 61.093 61.111 18.40 0.00 0.00 3.69
734 766 2.194597 GGCCATGGATGCGGGTAA 59.805 61.111 18.40 0.00 0.00 2.85
735 767 2.193536 GGCCATGGATGCGGGTAAC 61.194 63.158 18.40 0.00 0.00 2.50
745 777 3.799755 CGGGTAACGCTTGCTGCC 61.800 66.667 0.00 0.00 38.78 4.85
774 808 3.001330 GCGTGTTGGAATATGTAGACTGC 59.999 47.826 0.00 0.00 0.00 4.40
786 823 4.151258 TGTAGACTGCAGTTACGTACAC 57.849 45.455 22.65 11.26 0.00 2.90
989 1029 1.972660 ATCGCTTTCTTCCTCCCCCG 61.973 60.000 0.00 0.00 0.00 5.73
1235 1344 2.049063 GACGCTGCGGTTGACTCT 60.049 61.111 26.95 1.54 0.00 3.24
1236 1345 2.049063 ACGCTGCGGTTGACTCTC 60.049 61.111 26.95 0.00 0.00 3.20
1419 1540 2.232298 CTCAGCCCAAGGAGACCGTC 62.232 65.000 0.00 0.00 32.87 4.79
1758 1885 1.449956 GCTCAAGCAGAGGCAGAGG 60.450 63.158 8.09 0.00 44.86 3.69
1872 1999 2.161855 GGCAGTTGATCCATCACAACA 58.838 47.619 0.00 0.00 45.70 3.33
1889 2033 2.464157 ACAGTTGCTCCTCTGTAAGC 57.536 50.000 0.00 0.00 42.13 3.09
1933 2077 5.963176 TGCTGAAATCTGCAGAATACAAA 57.037 34.783 22.50 8.92 44.12 2.83
1948 2181 7.642669 CAGAATACAAACTTTGAGAAGAGCAA 58.357 34.615 8.55 0.00 36.69 3.91
1971 2204 2.627945 TGATCGGGTTCTTGTGTATGC 58.372 47.619 0.00 0.00 0.00 3.14
1981 2214 5.414454 GGTTCTTGTGTATGCTGTATTCCAA 59.586 40.000 0.00 0.00 0.00 3.53
2003 2236 7.440856 TCCAACTTTCCAACTTAATTGCAATTC 59.559 33.333 27.28 0.00 36.93 2.17
2004 2237 7.307930 CCAACTTTCCAACTTAATTGCAATTCC 60.308 37.037 27.28 0.00 36.93 3.01
2038 2274 5.391060 AAATATTCAGAACTTCGCTACGC 57.609 39.130 0.00 0.00 0.00 4.42
2058 2294 4.273969 ACGCTTGGACTTCAAACGATTTAA 59.726 37.500 8.24 0.00 44.85 1.52
2059 2295 5.048991 ACGCTTGGACTTCAAACGATTTAAT 60.049 36.000 8.24 0.00 44.85 1.40
2103 2342 3.078891 TGTGCAGCAAACCATGGTATA 57.921 42.857 20.12 0.00 37.77 1.47
2109 2348 3.023832 AGCAAACCATGGTATACAAGCC 58.976 45.455 20.12 1.15 38.18 4.35
2123 2363 0.250727 CAAGCCCGAAAAGGTCAGGA 60.251 55.000 0.00 0.00 38.74 3.86
2132 2372 4.192317 CGAAAAGGTCAGGAGATTTAGGG 58.808 47.826 0.00 0.00 0.00 3.53
2147 2387 5.719563 AGATTTAGGGCTCTAGCTAGGATTC 59.280 44.000 20.58 8.59 41.70 2.52
2148 2388 4.471078 TTAGGGCTCTAGCTAGGATTCA 57.529 45.455 20.58 0.00 41.70 2.57
2150 2390 3.868062 AGGGCTCTAGCTAGGATTCAAT 58.132 45.455 20.58 0.00 41.70 2.57
2152 2392 4.285775 AGGGCTCTAGCTAGGATTCAATTC 59.714 45.833 20.58 2.13 41.70 2.17
2153 2393 4.285775 GGGCTCTAGCTAGGATTCAATTCT 59.714 45.833 20.58 0.00 41.70 2.40
2160 2401 5.848406 AGCTAGGATTCAATTCTCCGTAAG 58.152 41.667 0.00 0.00 36.62 2.34
2172 2413 9.667107 TCAATTCTCCGTAAGAAAATATTCTGT 57.333 29.630 2.07 0.00 46.85 3.41
2173 2414 9.708222 CAATTCTCCGTAAGAAAATATTCTGTG 57.292 33.333 2.07 0.00 46.85 3.66
2174 2415 9.449719 AATTCTCCGTAAGAAAATATTCTGTGT 57.550 29.630 2.07 0.00 46.85 3.72
2175 2416 7.827819 TCTCCGTAAGAAAATATTCTGTGTG 57.172 36.000 0.00 0.00 45.19 3.82
2176 2417 7.608153 TCTCCGTAAGAAAATATTCTGTGTGA 58.392 34.615 0.00 0.00 45.19 3.58
2186 2427 3.876274 ATTCTGTGTGAGTGCGATACT 57.124 42.857 0.00 0.00 44.02 2.12
2187 2428 2.636768 TCTGTGTGAGTGCGATACTG 57.363 50.000 0.00 0.00 40.53 2.74
2219 2462 0.907486 TGTTGGAGATGGCTGAGGAG 59.093 55.000 0.00 0.00 0.00 3.69
2220 2463 1.198713 GTTGGAGATGGCTGAGGAGA 58.801 55.000 0.00 0.00 0.00 3.71
2221 2464 1.556911 GTTGGAGATGGCTGAGGAGAA 59.443 52.381 0.00 0.00 0.00 2.87
2222 2465 1.493861 TGGAGATGGCTGAGGAGAAG 58.506 55.000 0.00 0.00 0.00 2.85
2223 2466 0.106521 GGAGATGGCTGAGGAGAAGC 59.893 60.000 0.00 0.00 40.06 3.86
2233 2476 2.046892 GGAGAAGCCTTCGCAGCA 60.047 61.111 10.39 0.00 37.52 4.41
2234 2477 1.451028 GGAGAAGCCTTCGCAGCAT 60.451 57.895 10.39 0.00 37.52 3.79
2235 2478 1.028868 GGAGAAGCCTTCGCAGCATT 61.029 55.000 10.39 0.00 37.52 3.56
2236 2479 0.807496 GAGAAGCCTTCGCAGCATTT 59.193 50.000 3.11 0.00 37.52 2.32
2237 2480 0.524862 AGAAGCCTTCGCAGCATTTG 59.475 50.000 0.00 0.00 37.52 2.32
2238 2481 0.457337 GAAGCCTTCGCAGCATTTGG 60.457 55.000 0.00 0.00 37.52 3.28
2239 2482 0.895100 AAGCCTTCGCAGCATTTGGA 60.895 50.000 0.00 0.00 37.52 3.53
2240 2483 0.895100 AGCCTTCGCAGCATTTGGAA 60.895 50.000 0.00 0.00 37.52 3.53
2241 2484 0.733909 GCCTTCGCAGCATTTGGAAC 60.734 55.000 0.00 0.00 34.03 3.62
2242 2485 0.597568 CCTTCGCAGCATTTGGAACA 59.402 50.000 0.00 0.00 0.00 3.18
2243 2486 1.401931 CCTTCGCAGCATTTGGAACAG 60.402 52.381 0.00 0.00 42.39 3.16
2244 2487 1.536766 CTTCGCAGCATTTGGAACAGA 59.463 47.619 0.00 0.00 42.39 3.41
2245 2488 1.159285 TCGCAGCATTTGGAACAGAG 58.841 50.000 0.00 0.00 42.39 3.35
2246 2489 0.169672 CGCAGCATTTGGAACAGAGG 59.830 55.000 0.00 0.00 42.39 3.69
2247 2490 1.251251 GCAGCATTTGGAACAGAGGT 58.749 50.000 0.00 0.00 42.39 3.85
2282 2525 5.179182 GGTTTCATTACCAGTGCAAATTTGG 59.821 40.000 19.47 5.95 38.12 3.28
2289 2532 5.138125 ACCAGTGCAAATTTGGTAATGAG 57.862 39.130 19.47 6.68 43.15 2.90
2306 2549 8.428852 TGGTAATGAGCAGCAATTTACTCTATA 58.571 33.333 0.00 0.00 0.00 1.31
2359 2880 2.146073 GAACCCAACGCTGCAATGCT 62.146 55.000 6.82 0.00 0.00 3.79
2360 2881 2.126228 CCCAACGCTGCAATGCTG 60.126 61.111 6.82 7.34 0.00 4.41
2362 2883 2.807895 CAACGCTGCAATGCTGGC 60.808 61.111 13.79 12.86 0.00 4.85
2364 2885 2.567497 AACGCTGCAATGCTGGCTT 61.567 52.632 13.79 5.70 0.00 4.35
2365 2886 2.202570 CGCTGCAATGCTGGCTTC 60.203 61.111 13.79 0.00 0.00 3.86
2366 2887 2.202570 GCTGCAATGCTGGCTTCG 60.203 61.111 13.79 0.00 0.00 3.79
2367 2888 2.202570 CTGCAATGCTGGCTTCGC 60.203 61.111 6.82 0.00 0.00 4.70
2368 2889 2.984718 TGCAATGCTGGCTTCGCA 60.985 55.556 6.82 0.00 42.25 5.10
2369 2890 2.259204 GCAATGCTGGCTTCGCAA 59.741 55.556 0.00 0.00 41.26 4.85
2370 2891 1.804326 GCAATGCTGGCTTCGCAAG 60.804 57.895 0.00 0.00 41.26 4.01
2371 2892 1.582968 CAATGCTGGCTTCGCAAGT 59.417 52.632 1.28 0.00 41.26 3.16
2372 2893 0.731514 CAATGCTGGCTTCGCAAGTG 60.732 55.000 1.28 0.48 41.26 3.16
2375 2896 2.546494 GCTGGCTTCGCAAGTGTGT 61.546 57.895 0.00 0.00 31.11 3.72
2382 2903 1.728971 CTTCGCAAGTGTGTCATCCTC 59.271 52.381 0.00 0.00 39.48 3.71
2386 2907 1.537202 GCAAGTGTGTCATCCTCCAAC 59.463 52.381 0.00 0.00 0.00 3.77
2392 2913 2.437651 TGTGTCATCCTCCAACTTGTGA 59.562 45.455 0.00 0.00 0.00 3.58
2454 2979 7.253750 CGAAATTTGGCTGTTAGCATAATGTTC 60.254 37.037 0.00 7.22 44.75 3.18
2463 2988 7.360861 GCTGTTAGCATAATGTTCTGTTGTACA 60.361 37.037 0.00 0.00 41.89 2.90
2476 3005 5.977635 TCTGTTGTACATAGGTTCAGATGG 58.022 41.667 0.00 0.00 0.00 3.51
2481 3010 5.773091 TGTACATAGGTTCAGATGGACCTA 58.227 41.667 20.00 20.00 36.24 3.08
2494 3168 2.816411 TGGACCTAAGAATCTCACGGT 58.184 47.619 0.00 0.00 0.00 4.83
2507 3264 6.320418 AGAATCTCACGGTACACATGTATGTA 59.680 38.462 0.00 0.00 39.39 2.29
2508 3265 5.900865 TCTCACGGTACACATGTATGTAA 57.099 39.130 0.00 0.00 39.39 2.41
2559 3318 7.115805 CCAATTGTGAATGACATGTCTTTTCAG 59.884 37.037 29.24 21.45 35.09 3.02
2610 3369 2.738743 GGATGCAGGGGAAAGAAATGA 58.261 47.619 0.00 0.00 0.00 2.57
2611 3370 2.692041 GGATGCAGGGGAAAGAAATGAG 59.308 50.000 0.00 0.00 0.00 2.90
2612 3371 3.624777 GATGCAGGGGAAAGAAATGAGA 58.375 45.455 0.00 0.00 0.00 3.27
2613 3372 3.524095 TGCAGGGGAAAGAAATGAGAA 57.476 42.857 0.00 0.00 0.00 2.87
2614 3373 3.157087 TGCAGGGGAAAGAAATGAGAAC 58.843 45.455 0.00 0.00 0.00 3.01
2615 3374 3.157087 GCAGGGGAAAGAAATGAGAACA 58.843 45.455 0.00 0.00 0.00 3.18
2616 3375 3.057245 GCAGGGGAAAGAAATGAGAACAC 60.057 47.826 0.00 0.00 0.00 3.32
2617 3376 4.144297 CAGGGGAAAGAAATGAGAACACA 58.856 43.478 0.00 0.00 0.00 3.72
2618 3377 4.768968 CAGGGGAAAGAAATGAGAACACAT 59.231 41.667 0.00 0.00 0.00 3.21
2619 3378 4.768968 AGGGGAAAGAAATGAGAACACATG 59.231 41.667 0.00 0.00 0.00 3.21
2620 3379 4.766891 GGGGAAAGAAATGAGAACACATGA 59.233 41.667 0.00 0.00 0.00 3.07
2621 3380 5.243730 GGGGAAAGAAATGAGAACACATGAA 59.756 40.000 0.00 0.00 0.00 2.57
2622 3381 6.071165 GGGGAAAGAAATGAGAACACATGAAT 60.071 38.462 0.00 0.00 0.00 2.57
2623 3382 6.810182 GGGAAAGAAATGAGAACACATGAATG 59.190 38.462 0.00 0.00 0.00 2.67
2624 3383 7.373493 GGAAAGAAATGAGAACACATGAATGT 58.627 34.615 0.00 0.00 42.84 2.71
2646 3405 2.408032 GCACACATAAAATGGTTGTGCG 59.592 45.455 15.45 0.00 46.25 5.34
2650 3409 3.679025 CACATAAAATGGTTGTGCGCATT 59.321 39.130 15.91 3.14 34.89 3.56
2746 3527 2.325583 AGACCAAACTTTGAGCGTGA 57.674 45.000 2.87 0.00 0.00 4.35
2752 3533 3.184581 CCAAACTTTGAGCGTGAGAGTAC 59.815 47.826 2.87 0.00 0.00 2.73
2762 3543 3.058914 AGCGTGAGAGTACAAAATTGCAC 60.059 43.478 0.00 0.00 0.00 4.57
2775 3556 5.235616 ACAAAATTGCACTTCAGCTCAAATG 59.764 36.000 0.00 0.00 34.99 2.32
2810 3591 7.736893 ACTTGACTCAAAATAGTACAACTCCT 58.263 34.615 0.00 0.00 0.00 3.69
2858 3639 2.260481 GACTCGAGAAACCTAAAGGCG 58.740 52.381 21.68 0.00 39.32 5.52
2859 3640 1.000145 CTCGAGAAACCTAAAGGCGC 59.000 55.000 6.58 0.00 39.32 6.53
2860 3641 0.319083 TCGAGAAACCTAAAGGCGCA 59.681 50.000 10.83 0.00 39.32 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 0.318762 GGTACATGGCTCCGGAGATC 59.681 60.000 35.69 24.38 0.00 2.75
515 544 1.831652 CGCCCTCAAGTTCCTGGTCT 61.832 60.000 0.00 0.00 0.00 3.85
774 808 1.334054 GCACCTCGTGTACGTAACTG 58.666 55.000 0.00 0.00 40.80 3.16
1078 1187 4.082523 CATGTCAGGGTCGGCGGT 62.083 66.667 7.21 0.00 0.00 5.68
1291 1400 2.962569 CTCGGACTCGTGCTTCCA 59.037 61.111 0.00 0.00 37.69 3.53
1419 1540 3.476646 CAGACACGCTGCTGCTCG 61.477 66.667 14.03 11.92 37.90 5.03
1758 1885 0.548031 TCAGGATGGGGTGCATCTTC 59.452 55.000 0.00 0.00 36.16 2.87
1803 1930 2.354259 GTCTTCTTGACCATGGAGCTG 58.646 52.381 21.47 6.00 39.69 4.24
1827 1954 0.599204 GAAACTGCCTCGTGACCGAA 60.599 55.000 0.00 0.00 43.69 4.30
1843 1970 1.619432 GGATCAACTGCCCATGGGAAA 60.619 52.381 36.00 20.19 37.50 3.13
1872 1999 0.969894 ACGCTTACAGAGGAGCAACT 59.030 50.000 0.00 0.00 38.81 3.16
1927 2071 8.632679 TCAAATTGCTCTTCTCAAAGTTTGTAT 58.367 29.630 15.08 0.00 33.95 2.29
1928 2072 7.995289 TCAAATTGCTCTTCTCAAAGTTTGTA 58.005 30.769 15.08 2.74 33.95 2.41
1929 2073 6.866480 TCAAATTGCTCTTCTCAAAGTTTGT 58.134 32.000 15.08 0.00 33.95 2.83
1930 2074 7.149015 CGATCAAATTGCTCTTCTCAAAGTTTG 60.149 37.037 9.44 9.44 33.95 2.93
1931 2075 6.860023 CGATCAAATTGCTCTTCTCAAAGTTT 59.140 34.615 0.00 0.00 33.95 2.66
1932 2076 6.376978 CGATCAAATTGCTCTTCTCAAAGTT 58.623 36.000 0.00 0.00 33.95 2.66
1933 2077 5.106396 CCGATCAAATTGCTCTTCTCAAAGT 60.106 40.000 0.00 0.00 33.95 2.66
1948 2181 4.096382 GCATACACAAGAACCCGATCAAAT 59.904 41.667 0.00 0.00 0.00 2.32
1971 2204 9.410556 CAATTAAGTTGGAAAGTTGGAATACAG 57.589 33.333 0.00 0.00 40.30 2.74
2072 2309 4.260212 GGTTTGCTGCACATATACTACGTG 60.260 45.833 0.00 0.00 0.00 4.49
2075 2312 5.277974 CCATGGTTTGCTGCACATATACTAC 60.278 44.000 0.00 0.00 0.00 2.73
2093 2331 1.502690 TCGGGCTTGTATACCATGGT 58.497 50.000 23.55 23.55 0.00 3.55
2103 2342 0.537371 CCTGACCTTTTCGGGCTTGT 60.537 55.000 0.00 0.00 44.28 3.16
2109 2348 4.192317 CCTAAATCTCCTGACCTTTTCGG 58.808 47.826 0.00 0.00 39.35 4.30
2123 2363 4.750833 TCCTAGCTAGAGCCCTAAATCT 57.249 45.455 22.70 0.00 43.38 2.40
2132 2372 5.478407 GGAGAATTGAATCCTAGCTAGAGC 58.522 45.833 22.70 8.48 35.45 4.09
2147 2387 9.708222 CACAGAATATTTTCTTACGGAGAATTG 57.292 33.333 4.62 0.40 43.65 2.32
2148 2388 9.449719 ACACAGAATATTTTCTTACGGAGAATT 57.550 29.630 4.62 0.00 43.65 2.17
2150 2390 8.092068 TCACACAGAATATTTTCTTACGGAGAA 58.908 33.333 0.00 0.00 40.28 2.87
2152 2392 7.545965 ACTCACACAGAATATTTTCTTACGGAG 59.454 37.037 0.00 4.81 40.28 4.63
2153 2393 7.330946 CACTCACACAGAATATTTTCTTACGGA 59.669 37.037 0.00 0.00 40.28 4.69
2160 2401 5.530519 TCGCACTCACACAGAATATTTTC 57.469 39.130 0.00 0.00 0.00 2.29
2170 2411 0.316841 TGCAGTATCGCACTCACACA 59.683 50.000 0.00 0.00 36.86 3.72
2171 2412 3.122150 TGCAGTATCGCACTCACAC 57.878 52.632 0.00 0.00 36.86 3.82
2186 2427 5.227569 TCTCCAACAATTCTTAGAGTGCA 57.772 39.130 0.00 0.00 0.00 4.57
2187 2428 5.065731 CCATCTCCAACAATTCTTAGAGTGC 59.934 44.000 0.00 0.00 0.00 4.40
2192 2435 5.188434 TCAGCCATCTCCAACAATTCTTAG 58.812 41.667 0.00 0.00 0.00 2.18
2219 2462 0.457337 CCAAATGCTGCGAAGGCTTC 60.457 55.000 17.33 17.33 40.82 3.86
2220 2463 0.895100 TCCAAATGCTGCGAAGGCTT 60.895 50.000 0.00 0.00 40.82 4.35
2221 2464 0.895100 TTCCAAATGCTGCGAAGGCT 60.895 50.000 0.00 0.00 40.82 4.58
2222 2465 0.733909 GTTCCAAATGCTGCGAAGGC 60.734 55.000 0.00 0.00 40.52 4.35
2223 2466 0.597568 TGTTCCAAATGCTGCGAAGG 59.402 50.000 0.00 0.00 0.00 3.46
2224 2467 1.536766 TCTGTTCCAAATGCTGCGAAG 59.463 47.619 0.00 0.00 0.00 3.79
2225 2468 1.536766 CTCTGTTCCAAATGCTGCGAA 59.463 47.619 0.00 0.00 0.00 4.70
2226 2469 1.159285 CTCTGTTCCAAATGCTGCGA 58.841 50.000 0.00 0.00 0.00 5.10
2227 2470 0.169672 CCTCTGTTCCAAATGCTGCG 59.830 55.000 0.00 0.00 0.00 5.18
2228 2471 1.068055 CACCTCTGTTCCAAATGCTGC 60.068 52.381 0.00 0.00 0.00 5.25
2229 2472 2.507484 TCACCTCTGTTCCAAATGCTG 58.493 47.619 0.00 0.00 0.00 4.41
2230 2473 2.957402 TCACCTCTGTTCCAAATGCT 57.043 45.000 0.00 0.00 0.00 3.79
2231 2474 2.416431 GCATCACCTCTGTTCCAAATGC 60.416 50.000 0.00 0.00 0.00 3.56
2232 2475 2.165030 GGCATCACCTCTGTTCCAAATG 59.835 50.000 0.00 0.00 34.51 2.32
2233 2476 2.450476 GGCATCACCTCTGTTCCAAAT 58.550 47.619 0.00 0.00 34.51 2.32
2234 2477 1.909700 GGCATCACCTCTGTTCCAAA 58.090 50.000 0.00 0.00 34.51 3.28
2235 2478 3.650647 GGCATCACCTCTGTTCCAA 57.349 52.632 0.00 0.00 34.51 3.53
2245 2488 0.539438 TGAAACCCACAGGCATCACC 60.539 55.000 0.00 0.00 36.11 4.02
2246 2489 1.549203 ATGAAACCCACAGGCATCAC 58.451 50.000 0.00 0.00 34.78 3.06
2247 2490 2.307496 AATGAAACCCACAGGCATCA 57.693 45.000 0.00 0.00 35.99 3.07
2289 2532 9.237846 GTCCAATTTTATAGAGTAAATTGCTGC 57.762 33.333 12.10 0.00 44.50 5.25
2306 2549 7.016465 TCCAAGGATGAAAATCAGTCCAATTTT 59.984 33.333 9.77 0.00 38.64 1.82
2316 2559 5.474532 CAGTCAACTCCAAGGATGAAAATCA 59.525 40.000 0.00 0.00 0.00 2.57
2326 2847 1.142870 TGGGTTCAGTCAACTCCAAGG 59.857 52.381 0.00 0.00 34.01 3.61
2362 2883 1.728971 GAGGATGACACACTTGCGAAG 59.271 52.381 0.00 0.00 0.00 3.79
2364 2885 0.037326 GGAGGATGACACACTTGCGA 60.037 55.000 0.00 0.00 0.00 5.10
2365 2886 0.320683 TGGAGGATGACACACTTGCG 60.321 55.000 0.00 0.00 0.00 4.85
2366 2887 1.537202 GTTGGAGGATGACACACTTGC 59.463 52.381 0.00 0.00 0.00 4.01
2367 2888 3.131709 AGTTGGAGGATGACACACTTG 57.868 47.619 0.00 0.00 0.00 3.16
2368 2889 3.117888 ACAAGTTGGAGGATGACACACTT 60.118 43.478 7.96 0.00 0.00 3.16
2369 2890 2.439507 ACAAGTTGGAGGATGACACACT 59.560 45.455 7.96 0.00 0.00 3.55
2370 2891 2.549754 CACAAGTTGGAGGATGACACAC 59.450 50.000 7.96 0.00 0.00 3.82
2371 2892 2.437651 TCACAAGTTGGAGGATGACACA 59.562 45.455 7.96 0.00 0.00 3.72
2372 2893 3.126001 TCACAAGTTGGAGGATGACAC 57.874 47.619 7.96 0.00 0.00 3.67
2375 2896 4.074259 CAACATCACAAGTTGGAGGATGA 58.926 43.478 27.11 15.15 41.92 2.92
2386 2907 2.624838 AGGAAACAGCCAACATCACAAG 59.375 45.455 0.00 0.00 0.00 3.16
2392 2913 1.547372 GCATGAGGAAACAGCCAACAT 59.453 47.619 0.00 0.00 0.00 2.71
2398 2919 2.704725 TTTTCGCATGAGGAAACAGC 57.295 45.000 10.73 0.00 33.43 4.40
2438 2961 8.028540 TGTACAACAGAACATTATGCTAACAG 57.971 34.615 0.00 0.00 0.00 3.16
2454 2979 5.812642 GTCCATCTGAACCTATGTACAACAG 59.187 44.000 0.00 0.00 0.00 3.16
2463 2988 7.079048 AGATTCTTAGGTCCATCTGAACCTAT 58.921 38.462 7.40 0.00 35.10 2.57
2476 3005 4.157289 TGTGTACCGTGAGATTCTTAGGTC 59.843 45.833 10.58 5.76 33.58 3.85
2481 3010 4.537135 ACATGTGTACCGTGAGATTCTT 57.463 40.909 0.00 0.00 34.01 2.52
2530 3287 6.017400 AGACATGTCATTCACAATTGGAAC 57.983 37.500 27.02 1.20 38.97 3.62
2533 3290 6.924612 TGAAAAGACATGTCATTCACAATTGG 59.075 34.615 28.81 0.00 38.97 3.16
2559 3318 6.092122 GCCAATTTCCTGTAAATTTGTTAGCC 59.908 38.462 0.00 0.00 43.75 3.93
2622 3381 4.366586 CACAACCATTTTATGTGTGCACA 58.633 39.130 17.42 17.42 46.44 4.57
2623 3382 4.970472 CACAACCATTTTATGTGTGCAC 57.030 40.909 10.75 10.75 39.60 4.57
2627 3386 2.035193 TGCGCACAACCATTTTATGTGT 59.965 40.909 5.66 0.00 44.79 3.72
2628 3387 2.670479 TGCGCACAACCATTTTATGTG 58.330 42.857 5.66 0.97 45.54 3.21
2629 3388 3.591196 ATGCGCACAACCATTTTATGT 57.409 38.095 14.90 0.00 0.00 2.29
2630 3389 3.925299 TCAATGCGCACAACCATTTTATG 59.075 39.130 14.90 0.00 29.71 1.90
2631 3390 4.185467 TCAATGCGCACAACCATTTTAT 57.815 36.364 14.90 0.00 29.71 1.40
2632 3391 3.650070 TCAATGCGCACAACCATTTTA 57.350 38.095 14.90 0.00 29.71 1.52
2633 3392 2.522836 TCAATGCGCACAACCATTTT 57.477 40.000 14.90 0.00 29.71 1.82
2634 3393 2.029200 TGATCAATGCGCACAACCATTT 60.029 40.909 14.90 0.00 29.71 2.32
2635 3394 1.545136 TGATCAATGCGCACAACCATT 59.455 42.857 14.90 0.00 32.20 3.16
2636 3395 1.175654 TGATCAATGCGCACAACCAT 58.824 45.000 14.90 0.00 0.00 3.55
2637 3396 0.957362 TTGATCAATGCGCACAACCA 59.043 45.000 14.90 4.55 0.00 3.67
2638 3397 1.921887 CATTGATCAATGCGCACAACC 59.078 47.619 30.11 1.44 41.27 3.77
2650 3409 0.801872 CGCCGTTTCCACATTGATCA 59.198 50.000 0.00 0.00 0.00 2.92
2666 3425 2.096980 CGAAAAGGAGGGTAAATTCGCC 59.903 50.000 0.00 0.00 34.17 5.54
2723 3482 2.876550 ACGCTCAAAGTTTGGTCTAACC 59.123 45.455 15.47 0.00 39.22 2.85
2752 3533 5.464057 TCATTTGAGCTGAAGTGCAATTTTG 59.536 36.000 0.00 0.00 34.99 2.44
2762 3543 8.261492 AGTATGTACTTTCATTTGAGCTGAAG 57.739 34.615 0.00 0.00 34.33 3.02
2810 3591 6.563037 TTTGTGGCCTACTGGTATACATTA 57.437 37.500 3.32 0.00 35.27 1.90


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.